Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Animals, Год журнала: 2024, Номер 14(8), С. 1246 - 1246

Опубликована: Апрель 22, 2024

Cashmere goats are valuable genetic resources which famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic levels examined candidate associated with trait using whole-genome resequencing data from 123 Herein, Inner Mongolia goat presented lowest coefficient 0.0263. In total, 57,224 ROHs. Seventy-four islands containing 50 were detected. Certain meat, fiber milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); body size growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus identified, found (FGF5, DVL3, NRAS, KIT) length color. These findings enhance our comprehension foundations traits influenced by selective breeding. This contributes significantly future breeding, reservation use other breeds.

Язык: Английский

---

Leveraging Whole-Genome Resequencing to Uncover Genetic Diversity and Promote Conservation Strategies for Ruminants in Asia

Animals, Год журнала: 2025, Номер 15(6), С. 831 - 831

Опубликована: Март 13, 2025

Whole-genome resequencing (WGRS) is a critical branch of whole-genome sequencing (WGS), primarily targeting species with existing reference genomes. By aligning data to the genome, WGRS enables precise detection genetic variations in individuals or populations. As core technology genomic research, WGS holds profound significance ruminant studies. It not only reveals intricate structure genomes but also provides essential for deciphering gene function, variation patterns, and evolutionary processes, thereby advancing exploration mechanisms. However, still faces several challenges, such as incomplete inaccurate genome assembly, well annotation numerous unknown genes functions. Although can identify vast number variations, specific relationships between these phenotypes often remain unclear, which limits its potential functional studies breeding applications. performing on multiple samples, assembly challenges be effectively addressed, particularly regions high repeat content complex structural variations. accurately subtle among different populations further elucidate their associations traits, overcoming limitations providing more information research This review systematically summarizes latest applications analysis structures, diversity, economic adaptive while discussing faced by this technology. aims provide scientific foundation improvement conservation resources.

Язык: Английский

---

Genetic Diversity Estimation and Genome-Wide Selective Sweep Analysis of the Bazhou Yak

Animals, Год журнала: 2025, Номер 15(6), С. 849 - 849

Опубликована: Март 15, 2025

The Bazhou yak, a major native meat yak breed in Xinjiang, China, is renowned for its fast growth rate, strong adaptability, and particularly high intramuscular fat (IMF) content. However, limited knowledge regarding phylogenetic history genomic composition has hindered long-term conservation utilization. This study evaluated the genetic diversity, population phylogenetics, genome-wide selective sweep analysis (GWSA) of 100 newly obtained yaks through genome resequencing, as well 340 public genomes from nine other populations on Qinghai–Tibet Plateau. results revealed moderate lower inbreeding levels, rapid linkage disequilibrium (LD) decay yaks. Principal component (PCA) showed clear separation populations, indicating an independent population. Furthermore, less differentiation was found between Huanhu while ADMIXTURE common ancestral lineage yaks, important contribution Qinghai to GWSA identified total 833 selected genes using top 5% interaction windows both parameters (FST, Pi ratio, XP-EHH). A significant number these are related synthesis deposition, such MTOR, APOA1, GPAT4. In summary, this sheds light status distinctive features which facilitates our understanding basis IMF phenotype

Язык: Английский

---

Evaluating genomic inbreeding of two Chinese yak (Bos grunniens) populations

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Июль 24, 2024

Abstract Background Yaks are a vital livestock in the Qinghai-Tibetan Plateau area for providing food products, maintaining sustainable ecosystems, and promoting cultural heritage. Because of uncontrolled mating, it is impossible to estimate inbreeding level yak populations using pedigree-based approaches. With aims accurately evaluate two Chinese (Maiwa Jiulong), we obtained genome-wide single nucleotide polymorphisms (SNPs) by DNA sequencing calculated five SNP-by-SNP estimators ( $$\:{F}_{HOM}$$ , $$\:{F}_{L\&H}$$ $$\:{F}_{VR1}$$ $$\:{F}_{VR2}$$ $$\:{F}_{YAN}$$ ), as well segment-based runs homozygosity (ROH, $$\:{F}_{ROH}$$ ) homozygous-by-descent (HBD, $$\:{F}_{HBD}$$ ). Functional implications were analyzed positional candidate genes located within related genomic regions. Results A total 151,675 190,955 high-quality SNPs from 71 Maiwa 30 Jiulong yaks, respectively. had greater genetic diversity than terms allele frequency diversity. The could be genetically distinguished principal component analysis, with mean differentiation index (Fst) 0.0054. levels yaks consistently supported all estimators. Based on simple proportion homozygous lower was indicated three successfully sequenced old leather samples that may represent historical about generations ago. There 3304 ROH detected among samples, median length 1.97 Mb 1.0 Mb, 94 HBD segments found whereas 92 them belonged shortest class 10.9 Kb. estimates however, there no difference between yaks. Within regions significant Fst or enriched ROH, several pathways have been reported diverse production traits farm animals. Conclusions We evaluated populations. Although different resulted inconsistent conclusions their levels, our results helpful implement conservation utilization programs

Язык: Английский

---

Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data

Frontiers in Genetics, Год журнала: 2024, Номер 15

Опубликована: Июль 25, 2024

To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred variety through crossbreeding with exotic commercial breeds. This exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands.

Язык: Английский

---

Genomic insights into high-altitude adaptation and evolutionary dynamics of Indian yaks in the Trans-Himalayan region

Conservation Genetics, Год журнала: 2024, Номер 26(1), С. 49 - 62

Опубликована: Окт. 25, 2024

Язык: Английский

---

Genomic insight into X chromosome dynamics in high altitude adaptation of trans-Himalayan yaks

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Окт. 28, 2024

This study delves into the genomic foundations of high-altitude adaptation in Indian yaks, with a specific emphasis on X chromosome and its role traits related to production, reproduction, immunity. Utilizing whole-genome resequencing, we identified 319,015 high-quality chromosomal SNPs from 30 unrelated yaks 8 Jinchuan yaks. These were analyzed through various statistical methodologies, including composite likelihood ratio (CLR) statistics, Tajima’s D, iHS, F_ST, XP-EHH. Our findings highlight several genes associated adaptation, such as AIFM1, APOOL, ATRX, CHST7, DACH2, DGAT2L6, DIAPH2, EIF2S3B, CLR approaches. Additionally, GPR119, HS6ST2, MAGED1, MOSPD1, PQBP1, SLC25A14, SLC35A2, TIMM17B, WDR44 exhibited common selection signatures across F_ST XP-EHH methods. Unique loci each yak population uncovered chromosome, which are critical for adaptability, immunity, production traits. Notably, our regions containing RLIM gene Himachali is crucial Dosage Compensation chromosome. research offers new insights X-linked different populations, enhancing understanding mechanisms underlying adaptation.

Язык: Английский

---

Comparison of predictive ability of single-trait and multi-trait genomic selection models for body growth traits in Maiwa yaks

animal, Год журнала: 2024, Номер 18(11), С. 101350 - 101350

Опубликована: Окт. 4, 2024

Язык: Английский

---

Effect of miR-10a on the proliferation and differentiation of yak adipocyte precursors

Journal of Applied Genetics, Год журнала: 2024, Номер unknown

Опубликована: Дек. 24, 2024

Язык: Английский

---

Polymorphisms of TXK and PLCE1 Genes and Their Correlation Analysis with Growth Traits in Ashidan Yaks

Animals, Год журнала: 2024, Номер 14(23), С. 3506 - 3506

Опубликована: Дек. 4, 2024

The tyrosine protein kinase (

Язык: Английский

---